He doesn’t believe her until she lets Clarke out. Then he knows.
Miranda and Clarke are different people. Clarke’s face is sharper. When he asks Lye who he is, Clarke’s voice is deeper. When Clarke punches Lye in the face, his fist is broader. When Miranda comes back moments later, she apologizes and resets Lye’s nose with shaking fingers.
Lye pats her on the head and tells her it’s fine; it wasn’t her fault. He doesn’t understand Miranda and Clarke, but he does know what it’s like to be thirteen and alone with yourself.
Lye holds her while she cries.